A positive correlation (ρ = 0.758, P<0.01) is observed between autosomal heterozygosity and European ancestry (Figure 3). This increase in heterozygosity with higher European ancestry agrees well with expectations, based on the difference in mean diversity of European and Native American populations and their genetic differentiation, as measured by F ST (ρ = 0.786, P<0.01; See Methods). No significant correlation is seen between settlement size and genetic diversity or between settlement size and Native American ancestry (results not shown). Large differences in the variation of individual admixture estimates were seen across populations, with the variance in Native American ancestry between individuals ranging from 0.005 in Quetalmahue to 0.07 in Mexico City (Figure 4, Figure S1, and Table S2), an observation consistent with previous studies[31],[32].
